Effect of microsatellites on gene expression level and characteristics of expressed SSRs in poplars

doi:10.3969/j.jssn.1000-2006.2011.01.003

LIU Jingjing, DAI Xiaogang, WANG Jie, LI Shuxian, YIN Tongming

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2011, Vol. 35 ›› Issue (01) : 11-14.

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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2011, Vol. 35 ›› Issue (01) : 11-14. DOI: 10.3969/j.jssn.1000-2006.2011.01.003

Effect of microsatellites on gene expression level and characteristics of expressed SSRs in poplars

LIU Jingjing, DAI Xiaogang, WANG Jie, LI Shuxian, YIN Tongming

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Abstract

Microsatellites are highly repetitive sequences in eukaryotic genomes, which are commonly found in the intronic and intergenic regions. The genic regions also contain a number of microsatellites. Microsatellites are the most variable sequences in the genomes of different organisms. Mutation in microsatellite sequences will lead genes to produce shorter or completely different proteins. Thus, genes contains microsatellites would be strongly affected by selection. Low expression level is supposed to be one of the mechanisms that relax the selection against the corresponding genes and help their survival. In this paper, we analyzed 421 725 poplar ESTs in the publicly available NCBI database and detected 53 524 ESTs contained microsatellites, accounting for 1269 % of the investigated ESTs. Whereas in the 45 555 gene models annotated from the poplar genome sequences, 6 953 genes contained microsatellites, accounting for 1526 % of the total genes. Based on the frequency test between the EST database and gene database, microsatellites were found to occur with significantly lower frequency in ESTs than in annotated genes (p<001). Therefore, the results proved that the microsatellites frequency in expressed genes was lower than that of the expected level for all genes. The characteristics of microsatellite in ESTs were also explored in this study. The result showed that triplets were the most frequent microsatellites in ESTs. In this paper, the hypothesis that genes containing microsatellites might have low expression level is proposed for the first time. Meanwhile, a large number of ESTs are analyzed to verify this hypothesis. This study provides important evidences for us to understand the survival mechanism of microsatellites in genes.

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LIU Jingjing, DAI Xiaogang, WANG Jie, LI Shuxian, YIN Tongming. Effect of microsatellites on gene expression level and characteristics of expressed SSRs in poplars[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2011, 35(01): 11-14 https://doi.org/10.3969/j.jssn.1000-2006.2011.01.003

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